The continuing goal of this multifaceted project is to develop new physics-based methodologies and employ them to study complex biological structures and materials. Much of this work is undertaken to obtain deeper understanding of supramolecular entities such as biological membranes and cytoskeletal networks. Insights so gained then are used in inquiries of specific biological phenomena of medical import. For instance, we have developed techniques based on fluorescence correlation spectroscopy (FCS) and quantitative microscopy that make it possible for us to examine the movement of particles--varying in size from small metabolites to viruses--through concentrated polymer solutions and dense, interconnected polymer matrices. Some of these studies, which already have resulted in several publications, utilized models of non-biological origin, but similar techniques are now being employed to examine the movement of antibodies and viruses through vaginal secretions. In the latter case the goals are to understand how HIV and other viruses involved in sexually-transmitted diseases penetrate cervical mucus and other protective barriers to reach the cells which they infect. [unreadable] [unreadable] In a different study we used novel computer-based structural modeling, combined with dynamic light scattering (DLS), static light scattering (SLS), and small angle neutron scattering (SANS), to examine conformations of clathrin triskelions in solution. Clathrin is a major protein involved in receptor-mediated endocytosis (RME), a process whereby eucaryotic cells take up growth factors and metabolites, and also regulate surface-bound receptors for those materials. As such, receptor-mediated endocytosis is an integral component of many normal and abnormal growth processes and is involved in other aspects of cell and tissue development. Clathrin, along with other proteins, is a key constituent of the coats that surround membrane vesicles participating in RME and certain other intracellular trafficking processes of eucaryotic cells. In order to develop physical insights into the formation of the coats, we needed to determine how clathrin triskelia (heterohexameric complexes of clathrin heavy chains and clathrin light chains) change their shape when they leave solution to assemble into coat-like oligomers. We also developed a novel method, based on SANS, to assess the mechanical flexibility of the triskelions. The methods used in this work derive, in part, from our earlier investigations on nanoscopic tubulin rings formed in the presence of certain small peptides being considered as antimitotic agents for cancer therapy.[unreadable] [unreadable] The last example pertains to obtaining a basic understanding how physical boundaries influence spatial patterns that arise in concentrated ensembles of rod-shaped objects such as microtubules, amyloid plaques, and similarly-shaped biological assemblies. We constructed a biomimetic analog, composed of small hard rods confined within an enclosure of adjustable size and shape, that was subjected to mechanical shaking to mimic thermal excitation. The objective was to study the effects of steric interference between, e.g., microtubules, separately from other intermolecular interactions. We found that when the rods are confined to containers whose dimensions are of the same order of magnitude as the lengths of the rods, conditions exist where the rods self-organize and experience a density-dependent isotropic-nematic structure transition. This model pertains at an elemental level to microtubule involvement in cell division. Recently, in order to investigate the role of cytoplasmic factors that act as molecular crowders, we added small spheres to the ensemble of objects undergoing thermal excitation. New rod structures have been noted which, under certain conditions, differ dramatically from those seen in the absence of the spheres. In our earlier work we developed a continuum mathematical theory that explains how the observed patterns result from a competition between steric rod-rod interactions in the bulk and interactions of the rods with the container walls. An extension of that analysis is currently being developed to include the effects of the crowders.